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Ubiquitin signalling in DNA replication and repair

Key Points

  • DNA damage processing pathways involve checkpoints for damage sensing, repair pathways for damage removal and a system of damage tolerance to bypass lesions during DNA replication.

  • Non-degradative ubiquitin signalling, mediated by monoubiquitylation or polyubiquitylation through non-standard linkage, often involves the recruitment of downstream effectors that recognize relevant ubiquitylation targets by means of ubiquitin-binding domains. These domains sometimes show exquisite specificity for a particular type of chain geometry.

  • The signalling events at a DNA double-strand break are mediated by a ubiquitylation cascade involving the ubiquitin protein ligases RING finger protein 8 (RNF8) and RNF168, the modification of histone H2A and the formation of Lys63-linked polyubiquitin chains on as-yet-unidentified target proteins. Collectively, they promote the recruitment of the E3 ligase breast and ovarian cancer type 1 susceptibility protein (BRCA1), which is required for G2–M checkpoint arrest and initiates break repair by homologous recombination.

  • The Fanconi anaemia pathway is a replication-associated system for the processing of DNA interstrand cross links that culminates in the monoubiquitylation of the proteins Fanconi anaemia group D2 protein (FANCD2) and FANCI, resulting in their recruitment to chromatin and the initiation of recombination-mediated repair.

  • Post-translational modification of the replication clamp protein proliferating cell nuclear antigen (PCNA) by monoubiquitylation and Lys63-linked polyubiquitylation controls replicative lesion bypass by translesion synthesis and an error-free, recombination-like mechanism, respectively. In budding yeast, PCNA is also subject to sumoylation, which facilitates the ubiquitin-dependent pathways by inhibiting unscheduled recombination events.

Abstract

Post-translational modification by ubiquitin is best known for its role in targeting its substrates for regulated degradation. However, non-proteolytic functions of the ubiquitin system, often involving either monoubiquitylation or polyubiquitylation through Lys63-linked chains, have emerged in various cell signalling pathways. These two forms of the ubiquitin signal contribute to three different pathways related to the maintenance of genome integrity that are responsible for the processing of DNA double-strand breaks, the repair of interstrand cross links and the bypass of lesions during DNA replication.

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Figure 1: Processing of DNA damage.
Figure 2: Ubiquitin signalling at DNA double-strand breaks.
Figure 3: The Fanconi anaemia pathway.
Figure 4: Ubiquitin-dependent DNA damage bypass.

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Correspondence to Helle D. Ulrich or Helen Walden.

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Glossary

Ubiquitin-binding domain

(UBD). A domain that mediates non-covalent interactions with ubiquitin. UBDs are usually found in downstream effectors that selectively interact with ubiquitylated target proteins and come in various different types (reviewed in Ref. 9), such as α-helical motifs in UBM, UIM and MIU, or zinc fingers, as in UBZ.

Replication fork

The part of replicating DNA in which the two strands are being separated and DNA synthesis is occurring to generate two copies of the parental DNA.

Homologous recombination

Genetic recombination process in which nucleotide sequences are exchanged between two strands of identical or similar DNA. This pathway is widely used in repairing DSBs.

Non-homologous end joining

A means to repair DSBs that is alternative to homologous recombination and involves direct ligation of the break ends without the need for a homologous template.

Base excision repair

A DNA repair pathway that is primarily responsible for removing small, non-helix-distorting base lesions that affect only one strand, such as alkylation or oxidative damage.

Nucleotide excision repair

A pathway responsible for the removal of bulky, helix-distorting lesions that affect only one strand, involving the excision of a lesion-containing oligonucleotide and the resynthesis of the affected region.

FHA

A 65–100-residue phosphorylation-specific protein–protein interaction motif that was first identified in forkhead transcription factors. It is often found in proteins that also contain BRCT repeats.

BRCT

A 90-residue phosphate-binding tandem domain that interacts with specific motifs in their phosphorylated form, such as in γ-H2AX.

RING

A zinc-binding protein–protein interaction motif found in RING-type E3 enzymes that scaffolds two zinc ions and forms the hallmark of the largest class of E3 ligases.

HECT

A domain with a catalytic Cys residue (found in a class of E3 enzymes) that forms a thioester intermediate during ubiquitin transfer to the substrate protein.

WD40 repeat

Repeat of 40 amino acids with a characteristic central Trp–Asp motif.

Translesion synthesis

The processing of a lesion-containing replication template by a damage-tolerant polymerase that inserts either correct or inappropriate nucleotides opposite the lesion, thus potentially contributing to damage-induced mutagenesis.

26S proteasome

A large multisubunit protease complex that selectively degrades polyubiquitylated proteins.

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Ulrich, H., Walden, H. Ubiquitin signalling in DNA replication and repair. Nat Rev Mol Cell Biol 11, 479–489 (2010). https://doi.org/10.1038/nrm2921

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